In medical imaging of prepared tissue samples for microscopic analysis, there is the need to first locate the tissue on a solid support. In order to image the tissue sections most efficiently, the system must first know exactly where tissue is located on the solid support. In the simplest description, the system must look at the entire solid support and identify which sections are tissues, which are glass, label and debris. The tissue location is then converted to a region envelope. The coordinates of the region are then mapped in the position space of the microscope stage. This allows the microscope motion to be programmed to cover the appropriate areas of the solid support, and avoid areas of waste where no tissue exists. This technique is often referred to as scan planning.
While it may be preferred to extract information directly about the location of tissue during analysis, the use of standard fiducials is problematic due to slide-to-slide and operator-to-operator variability. Tissue-based scan planning is often preferred as it allows more repeatable and reliable plans while avoiding requirements for special slides or particular mounting techniques.
Typical approaches for scan planning involve performing a coarse scan of the complete solid support at a relatively low magnification (e.g. 1.25×) in order to localize the tissue which is digitized and reconstructed to provide a user with a magnified image of the specimen prior to a more detailed analysis.
Current methods often rely on color or texture to differentiate tissue from the solid support. There are several potential problems with these methods because they are likely to catch ink or stray marks on the slide, as well as the fiducial cross-hatching on the edges of some slides. In the case of tissue labeled with fluorescent dyes, the image acquisition time is often slow; there is the possibility that a stained tissue sample may undergo photo bleaching before the imaging process is complete. Further, when a tissue is stained with fluorescent dyes, often the dye necessarily localizes to a specific sub-region of the tissue and does not completely cover the tissue, making it difficult to accurately discern tissue from non-tissue as is possible when using other dyes such as hematoxylin and eosin (H&E) which are visible in brightfield imaging. Therefore fluorescent dyes necessitate other methods of detection. Finally, current methods do not typically work well for unstained tissue sections, as thin tissue sections are essentially transparent in visible light and therefore do not provide enough signal information to process accurately.